8CQ4 | pdb_00008cq4

Bifunctional cyclohexadienyl dehydratase/chorismate mutase from Janthinobacterium sp. HH01

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HPQ	cyclohexadienyl dehydratase from Pseudomonas aeruginosa
experimental model	PDB	6CNZ	chorismate mutase from Burkholderia thailandesis

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	10% w/v PEG 20 000 20% v/v PEG MME 550 0.03 M Sodium nitrate 0.03 M Disodium hydrogen phosphate 0.03 M Ammonium sulfate 0.1 M MES/imidazole pH 6.5 (Morpheus buffer 1) 3.5 mg/mL protein in 20 mM TRIS-HCl, pH 8

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.584	α = 90
b = 73.985	β = 90
c = 131.22	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.976	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.65	65.6	93	0.998	14.1	12.7		35076

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.83	54.6		0.542	1.6	9.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	65.6	35076	1717	72.148	0.194	0.1917	0.2	0.2453	0.25	28.766

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.076			0.113		-0.036

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.359
r_dihedral_angle_6_deg	15.212
r_dihedral_angle_2_deg	10.515
r_dihedral_angle_1_deg	6.372
r_lrange_it	6.306
r_lrange_other	6.306
r_scangle_it	5.382
r_scangle_other	5.381
r_mcangle_it	3.874
r_mcangle_other	3.874
r_scbond_it	3.609
r_scbond_other	3.609
r_mcbond_it	2.916
r_mcbond_other	2.91
r_angle_refined_deg	1.658
r_angle_other_deg	0.545
r_symmetry_xyhbond_nbd_other	0.405
r_symmetry_nbd_refined	0.27
r_nbd_refined	0.222
r_nbd_other	0.215
r_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.11
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3066
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing